Methods for removal of specific seed tissue or structure for seed analysis

ABSTRACT

A method for reducing resources for selecting seed to be produced in commercial quantities or for research is disclosed. Samples of seed which are candidates for selection are collected and given an identifier. Specific tissue or structure from candidate seed is removed. A test or analysis is performed on the candidate seed or the removed tissue or structure. Results of the test or analysis are recorded and correlated to the seed&#39;s identifier. The results are evaluated and a decision is made whether to select a candidate seed for commercial production or for research. Time, space, and labor associated with growing plants in an experimental plot or greenhouse and taking tissue samples from growing plants is saved.

RELATED APPLICATIONS

This application claims priority under 35 U.S.C. §119 to provisionalapplication Ser. Nos. 61/090,950 filed Aug. 22, 2008 and 61/092,863filed Aug. 29, 2008, which applications are hereby incorporated byreference in their entirety.

I. BACKGROUND

A. Field of the Invention The present invention relates to methods foranalyzing seed and to make decisions about the seed and its subsequentuse based on the analysis, and in particular, methods for efficient andeffective removal of specific seed tissue or structure to enable testingand analysis of the seed or its removed tissue or structure.

B. Problems in the Art

A primary goal of seed companies is to develop seed that grow intoplants that are commercially desirable to crop producers. Seed companiesdevote substantial resources towards research and development ofcommercially desirable seed.

Conventional research and development techniques tend to be laboriousand require vast amounts of land and space. All or much of the seedinvolved in the research is planted in research plots. After plantsemerge from the seed, tissue samples from each plant are acquired. Thetissue samples are transported to a laboratory to deduce informationneeded for the research and development of the seed and plants from theseed.

These methods are well-known in the industry. The resource costs ofland, labor, and machinery are substantial.

Thousands, if not hundreds of thousands, of acres of experimental plotscan be utilized. Appropriate numbers of workers and machinery to till,plant, maintain, obtain plant tissue samples, transport to the lab, andconduct analyses at the lab, are substantial. Time is also a factor andcost. Decisions about whether a plant and its seed should be used forproducing commercial quantities or seed, or should be used in furtherresearch, have to wait until tissue samples from emerged plants arepossible.

A typical process is as follows. Seed of known parentage, phenotype, orgenotype are planted in experimental plots outdoors or in greenhouses. Astatistically valid number of plants must be grown in the fields orgreenhouses. This involves substantial physical space and labor. Afterthe plants have emerged, tissue samples are taken from the plant. Testsare conducted to identify the genetic makeup or other characteristics ofthe sample. This process, of course, takes substantial time. The plantsmust grow to a point where a tissue sample can nondestructively betaken. The samples must be carefully handled and taken to a laboratory.Genetic testing must be conducted before identification of a gene ofinterest can be made.

It could be beneficial to have a process whereby access to and testing(genetically or otherwise) of relevant genetic material, or tissues,parts, or structures, could be gained without having to grow plants fromthe seed. As can be appreciated by the skilled artisan, savings inlabor, time and space could be substantial.

Obtaining a tissue sample with relevant cellular material from mostgrowing plants is not difficult. Conventionally, a relatively smallportion or sample of tissue from a growing plant is removed with a tool(e.g., manually operated leaf punch). If properly done, the removal ofthe samples is non-destructive, in the sense that a small leaf punchnormally does not materially affect the health or viability of theplant. A leaf punch, for example, is used to remove relevant cells foranalysis of the plant. Although such leaf samples are not destructive ofthe plant and are relatively easy to transport to the laboratory and tostore, obtaining a plant tissue sample from the normal quantity ofplants in seed company experimental plots remains a huge commitment oflabor and time. It requires going to each plant in the growing locationsand acquiring the leaf sample.

The seed from which the test plot plants are grown also has relevantcellular material. It is quite another matter, however, to gain accessto it and perform tests or assays on it without materially affecting theseed's viability or germination potential. The relatively small size ofmost seed, and its parts, is one reason. Another is that relevant tissueor structure in some seed is only a subset of the whole seed, and manytimes is inside an outer cover. This makes it difficult to gain accessto or acquire only relevant material. Furthermore, some seed have amake-up which makes non-destructive sampling difficult. The toughexterior layer or tissue, the pericarp, of corn seed is an example. Itis difficult to remove without using methods that destroy or damage theseed. Still further, all of these issues are antagonistic to highthroughput access to and sampling of multiple seed. Precise removal ofspecific tissue or structure from a small object to gain access to otherspecific tissue or structure, and doing so efficiently, presentssignificant challenges.

Therefore, a need exists in the industry to materially reduce theresources used for evaluating plants and their seed for potentialcommercial production or further use in plant and seed research anddevelopment. There is also a need in the art for methods to remove fromand/or gain access to specific tissues or structures of a seed,including in a non-destructive and relatively high throughput way.

II. BRIEF SUMMARY

One aspect of the invention is a method for reducing resources forselecting seed to be produced in commercial quantities. Seed which arecandidates for possible selection are collected and each is given anidentifier. Specific tissue or structure from a single candidate seed isremoved to expose or gain access to specific tissue, part(s), orstructure of that candidate seed, or to separate and collect specifictissue, part(s), or structure. A test or analysis is performed on theexposed tissue or the removed tissue of the candidate seed. Results ofthe test or analysis are evaluated and a decision can be made whether toselect that candidate seed type for, e.g., commercial production. Theresults can be recorded and associated with the seed's identifier. Themethod avoids the time, space, and labor of growing plants in anexperimental plot or greenhouse and taking tissue samples from growingplants. Decisions can be made quickly with relatively high throughputdirectly from a seed.

An method according to an aspect of the invention can include a seedholder and a tool which cooperate to allow the removal of specific seedtissue or structure. The seed holder isolates a seed from other seed andpresents it to the tool for tissue removal. Either the exposed tissue inthe seed, or removed tissue from the seed can then be tested.

In another aspect of the invention, a method comprises a controlledlaser to ablate, cut, separate, or remove tissue, part(s), or structurefrom seed to obtain or expose desirable parts of the seed in arelatively rapid and accurate manner, while not materially affectingseed viability or germination potential. Relevant exposed part(s) ortissue of the seed can be tested or analyzed, and/or removed part(s) ortissue of the seed can be tested or analyzed.

In another aspect, a method comprises automated steps or automatedcomponents in which plural candidate seed can be moved to a tissueremoval station, have specific tissue, part(s), or structure removed,and have either (or both) the remaining seed or its removed tissuetested and evaluated. The test(s) or evaluation (s) can include, but arenot limited to, genetic, physical, or chemical analysis on a cellular,molecular, or nanoscale level.

III. BRIEF DESCRIPTION OF THE DRAWINGS A. Figures

FIG. 1 is a flow chart of a general methodology according to one aspectof the present invention.

FIG. 2 is a block diagram illustrating apparatus and functionalityrelative to a first specific Example 1 of practicing the method of FIG.1.

FIG. 3 is a diagrammatic partial perspective view of one aspect of theinvention according to Example 1.

FIGS. 4A-C are plan views of plate 18 of FIG. 3.

FIG. 4D is an enlarged partial sectional view of one of the wells fromplate 18, further showing the positioning of a corn seed in the well.

FIGS. 5A and B are enlarged plan and side sectional views of a typicalcorn seed.

FIG. 6A illustrates one way to deposit a plurality of corn seed incorresponding individual wells of a plate 18 prior to laser ablation.

FIG. 6B diagrammatically illustrates an alternative way of depositing asingle seed in each of the wells of plate 18.

FIG. 7 is a plan view diagram of a software template which allows designof an ablation area for each well of plate 18.

FIG. 8A is an enlarged diagrammatic side elevation view illustratinglaser ablation which removes tissue from the seed, leaving a cavity ofrectangular prism shape on one surface of the seed.

FIG. 8B is an enlarged top plan view of the laser ablated seed of FIG.8A.

FIGS. 9A-C illustrate various views of a rectangular prism cavity 80from laser ablation of a seed, in particular, removal of a portion ofthe pericarp to expose or remove some of the seed endosperm.

FIGS. 10A-C show an alternative ablation pattern for a seed, namely acavity having a combination of rectangular prism cavities.

FIGS. 11A-C show a still further alternative example of a pattern thatcan be laser ablated into a single kernel, here a first channel in arectangular shape and a second channel in a rectangular shape spacedfrom and around the first channel.

FIGS. 12A-C show various views of another example of a laser-ablatedpattern in a seed, here a rectangular prism through the pericarp toexpose or ablate a portion of the seed embryo.

FIGS. 13A-C are similar to FIGS. 10A-C but illustrate control of a laserto create a more circular pattern.

FIGS. 14A-C are similar to FIGS. 11A-C but illustrate control of a laserto create circular patterns.

FIG. 15 is a diagrammatic illustration of an Example 2 according to analternative embodiment of the present invention, where debris from laserablation of a seed is collected by vacuum into a container where thedebris or removed tissue is tested or analyzed as opposed to exposedtissue in the seed.

FIG. 16 is a partial sectional, side elevation view of a methodologyaccording to Example 2.

FIG. 17 is a reduced in scale diagrammatic illustration of an optionalvacuum system to remove debris generated by laser ablation of a set ofseed each positioned in a well of a tray or plate.

FIG. 18 is a diagrammatic illustration of an optional seed cutter usinga laser for cutting, and a seed holding and orientation system based onmagnetism.

IV. DETAILED DESCRIPTION A. Overview

For a better understanding of the invention, several exemplaryembodiments of the present invention will be described in detail.Frequent reference will be taken to the accompanying drawings. Referencenumerals and letters will be used to indicate certain parts andlocations in the drawings. The same reference numerals or letters willbe used to indicate the same or similar parts and locations throughoutthe drawings unless otherwise indicated.

B. Context of the Exemplary Embodiments

The exemplary embodiments described will be primarily in the context ofcorn and corn seed. It is to be understood, however, that this is butone example of a seed that could be utilized with aspects of the presentinvention. Additionally, the context of the primary exemplaryembodiments is removal of a relatively small amount of tissue orstructure of a corn kernel to (a) expose and test specific internaltissue(s) or structure(s) of the seed or (b) test the removed tissue orstructure. The removal is intentionally controlled to minimize or avoiddetrimental effects to seed viability or germination potential. However,the invention could be used to remove substantially more tissue, even tothe point of threatening or destroying seed viability, if an applicationrequires the same.

The embodiments can be applied in analogous ways to other seed. Examplesinclude but are not limited to oat, soybean, wheat, rye, rice, canola,Brassica sp., sorghum, sunflower, barley, millet, alfalfa, cotton,peanut, flax, safflower, palm, olive, castor bean, coconut, millet,arabidopsis, tobacco, or sorghum seed.

C. Exemplary General Method

FIG. 1 illustrates a general exemplary method 200 according to oneaspect of the present invention. Method 200 allows selection of seed touse for further research or commercial production without growing plantsfrom the seed and testing living tissue of the plants. The method canavoid use of land, labor, time, equipment, and materials for growingplants from the seed to then acquire non-destructive samples to analyzefor selection decisions. The method can be non-destructive of the seed,allow relatively high throughput of multiple samples, and besubstantially automated. Method 200 comprises the following steps.

A plurality of corn kernels of different genotype and/or different cornvarieties are analyzed and compared for the purpose of identifying andselecting whether any will be utilized for further research anddevelopment or planted to produce commercial or research scalequantities. The method applies as well to other seed specific tests oranalysis, such as will be apparent to the skilled artisan.

1. Identification of Candidate Seed (Steps 201/202)

One or more factors are used to decide which seed will be a candidateseed for evaluation (FIG. 1, step 201). In this example, a set of aplurality of individual candidate seed, each having a different trait orgenotype and/or corn variety, are pre-selected. Each candidate seed isisolated from the other candidates but with association to informationfrom which the candidate seed can be identified (step 202). Thatidentity can be maintained with each seed through the method.Identification of each seed can be by specific information and/or bysome code related to information about or identity of the seed. It canbe recorded or stored (e.g., in a computer in a database). Other methodsare possible.

Pre-selection of candidate seed can be based on any of a number offactors or criteria. Research scientists select the factors or criteria.Examples of types of factors and criteria are commonly known in the art.Some are genotype, phenotype, parentage, traits, or characteristics.Further discussion of these factors or criteria can be found in suchreferences as: (a) Chahal, G. S & Gosal, S. S., 2002. “Principles andProcedures of Plant Breeding”, Alpha Science International, UnitedKingdom; (b) Falconer, D. S. 1989. “Introduction to QuantitativeGenetics”. 3rd Ed. Longman. Burnt Mill; and (c) Frisch, M. & Melchinger,A. E., 2005. “Selection Theory for Marker-assisted Backcrossing.”Genetics: Published Articles Ahead of Print, published on Mar. 31, 2005as 10.1534/genetics.104.035451; which are incorporated by referenceherein.

2. Isolation of Single Seed (Step 204)

A single candidate seed is isolated by any of a number of ways topresent it for removal of specific tissue (FIG. 1, step 204) to gainaccess to or expose certain specific tissues(s), part(s), orstructure(s) of that seed for testing, or collect the removed tissue fortesting. For purposes of this description, tissue(s), part(s), orstructure(s) of a seed will collectively sometimes be referred to astissue. One example of isolation is to place the candidate seed into acavity or well. Another is to grasp, hold, or restrain the seed by or tosome device (e.g., with a vacuum; by clamping action). Another is toapply a substance to the seed which is attracted to or held to a surfaceor member (e.g., adhesive; magnetism). Others are possible. The basicfunction is to hold the seed for accurate and efficient tissue removaland isolate the seed from others, while maintaining identity of theseed.

3. Removal of Specific Tissue (Step 205)

Tissue of the seed is removed from a specified location of the seed. Anumber of methods can be used. It can be useful, in certain of themethods, to first orient the seed in a certain manner. This can assistin removal of the specified tissue.

An example of tissue removal is with use of a laser (see FIG. 3). Asdescribed in more detail later, a laser can be precisely controlled inintensity. It also can be focused to a beam width that can beeffectively used for removing only a relatively small area of tissuefrom one side of a seed, and to a relatively small, controlled depth.

The laser beam can be operated in a variety of ways to effect tissueremoval. An example is programmable raster scanning. The beam iscontrolled to move at a programmed speed and direction relative to thearea to be removed.

The laser beam can be focused upon and moved with precision across theseed to ablate the portion of the seed it strikes and remove tissue.Ablation is defined by one source to remove or destroy especially bycutting, abrading, or evaporating (vaporizing) (Merriam-Webster OnLineDictionary 2007). Another source describes it as removal of materialfrom the surface of an object by vaporization, chipping, or othererosive processes (WIKIPEDIA. “Ablation” article [online], [retrieved on2008-08-18]. Retrieved from the Internet<URL:(http://en.wikipedia.org/wiki/Ablation>). As used herein, ablationrefers to such actions, or to analogous actions that remove or separatesuch seed tissue from the seed. In some instances, this resultsessentially in a candidate seed having some tissue removed to expose orallow access to internal tissue. The ablation may result in one piece orjust a few pieces of removed tissue (more in the sense of cutting orchipping). Alternatively, the ablation may result in the removed tissuebeing essentially debris (more in the sense of fragments or very smallparticles, even dust-like, from abrasion, erosive processes, or thelike). Alternatively, the ablation may result in the removed materialevaporating, sublimating, or forming a plasma.

A laser can function in these manners to remove specific tissue from theseed. As mentioned earlier, removed tissue can be collected for testingor analysis. Alternatively, testing or analysis of the remaining seedcan be conducted as the tissue removal can be designed to expose orallow access to tissue in the remaining seed.

In the case of corn, a laser beam can be controlled to remove an area ofthe pericarp to gain non-destructive access to underlying seedtissue(s), part(s), or structure(s) of interest. As illustrated in thecross sections of a corn kernel in FIGS. 5A and B, two possibilities arethe embryo 74 or the endosperm 76. The embryo 74 is usually at or nearthe tip cap end 67 of the seed and nearer one flat side of the seed thanthe other. The endosperm extends roughly along the entire opposite sidefrom the embryo side, but broadens out and occupies most of the interiorat the seed end opposite the tip cap. Thus, access to either embryo orendosperm is possible from one flattened side of the corn seed, withoutremoval of much intervening seed tissue. In particular, either embryo orendosperm can be exposed by essentially removal of a small amount of theouter seed coat or pericarp.

By initialization and calibration, a laser can be controlled to removeonly enough of the pericarp to gain sufficient internal access that anassay can be conducted on certain desired internal tissue or structure.The laser can also be controlled to remove only enough of the pericarpto gain sufficient access to the interior without materially affectingthe viability or germination potential of the seed.

By empirical testing, the power and speed of the beam can be adjusted tomeet those goals. As illustrated in FIGS. 8-14, the area removed istypically a fraction of the total area of one side of the kernel. Atypical depth of ablation would be through the pericarp and then justenough to expose but not destroy the target internal tissue orstructure. By appropriate set up, calibration, and empirical testing,operation of the laser can be non-destructive of the seed by controllingheat generated by the laser, removing only certain seed tissue, andremoving only so much seed tissue to gain access to underlying tissue orstructure of interest. Such operation is non-destructive in the sensethat it does not usually materially reduce viability of the remainingseed or its germination potential. It has been found that a laserincludes the benefits of high precision in control of movement, area anddepth of ablation, and its efficiency.

However, other methods of non-destructive seed tissue removal arepossible. One example is a water jet or abrasive jet (e.g., commerciallyavailable from Berkeley Chemical Research, Inc., Berkeley, Calif.94706-026; Flow International Corporation, Kent, Wash. USA; and others).Another is a grinding tool (e.g., Dremel brand MultiPro™ rotary tool)with appropriate sized bit and tip (e.g., engraving, cutting, grinding,carving, sanding, or routing bit tip available at a variety ofcommercial locations or on-line from Robert Bosch Tool Corporation).Additional description and illustration of alternative tools or methodsof removing tissue from seed are set forth in U.S. application Ser. No.11/939,402, filed Nov. 13, 2007, which application is assigned to theowner of the present application and incorporated by reference herein inits entirety. The system of FIG. 18, also described in more detail inapplication Ser. No. 11/939,402, provides a specific example of removingtissue from a seed by cutting off a single piece of the seed. In theexample of FIG. 18, the cutting tool is a laser.

4. Seed Specific Analysis (Step 206)

A number of analyses can be applied to the seed after tissue has beenremoved, or to the removed tissue from the seed. One example is geneticanalysis. By methods known in the art, exposure of the embryo, forexample, allows assays to be performed for detection of nucleic acidsfrom which genetic information about the seed can be derived.

An example of one such method is as follows. The ablated seed can beimmersed in a polymerase chain reaction (PCR) mixture in preparation forany number of PCR analyses. A detector can generate a signalrepresentative of some aspect of the PCR from which genotyping can bederived. Details of such a signal and its use are well known. A varietyof PCR detectors are commercially available. One example is an opticaldetector for PCR (e.g., Chromo4™ Real-Time PCR Detector from Bio-RadLaboratories, Inc., Life Science Research Group, 2000 Alfred NobelDrive, Hercules, Calif. 94547 USA).

Nucleotide sequences can be used to isolate corresponding sequences fromother organisms, particularly other plants, more particularly othermonocots. In this manner, methods such as PCR, hybridization, and thelike can be used to identify such sequences, or fragments thereof, basedon their sequence homology.

In a PCR approach, oligonucleotide primers can be designed for use inPCR reactions to amplify corresponding DNA sequences from cDNA orgenomic DNA extracted from any plant of interest. Methods for designingPCR primers and PCR cloning are generally known in the art and aredisclosed in, inter alia, Innis et al., eds. (1990) PCR Protocols: AGuide to Methods and Applications (Academic Press, New York); Innis andGelfand, eds. (1995) PCR Strategies (Academic Press, new York); andInnis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, NewYork), herein incorporated by reference in their entirety. Known methodsof PCR include, but are not limited to, methods using paired primers,nested primers, single specific primers, degenerate primers,gene-specific primers, vector-specific primers, partially-mismatchedprimers, and the like.

In hybridization techniques, all or part of the nucleotide sequence isused as a probe that selectively hybridizes to other correspondingnucleotide sequences present in a population of cloned genomic DNAfragments or cDNA fragments (i.e., genomic or cDNA libraries) from achosen organism. The hybridization probes may be genomic DNA fragments,cDNA fragments, RNA fragments, or other oligonucleotides, and may belabeled with a detectable group such as ³²P or any other detectablemarker. Methods for preparation of probes for hybridization and forconstruction of genomic libraries are generally known in the art.

To achieve specific hybridization under a variety of conditions, suchprobes include sequences that are unique and are generally at leastabout 10 nucleotides in length or at least about 20 nucleotides inlength. Such probes may be used to amplify corresponding sequences froma chosen plant by PCR. This technique may be used to isolate additionalcoding sequences from a desired organism, or as a diagnostic assay todetermine the presence of coding sequences in an organism. Hybridizationtechniques include hybridization screening of plated DNA libraries(either plaques or colonies).

Hybridization of such sequences may be carried out under stringentconditions. The terms “stringent conditions” or stringent hybridizationconditions” are intended to mean conditions under which a probe willhybridize to its target sequence to a detectably greater degree than toother sequences (e.g., at least 2-fold over background). Stringentconditions are sequence-dependent and will be different in differentcircumstances. By controlling the stringency of the hybridization and/orwashing conditions, target sequences that are 100% complementary to theprobe can be identified (homologous probing).

Another analysis could be cellular level analysis. An example withrespect to corn is described at Gabriella Consonni et al., “GeneticAnalysis as a Tool to Investigate the Molecular Mechanisms UnderlyingSeed Development in Maize”, Annals of Botany 2005 96(3):353-362, whichis incorporated by reference herein.

A still further example is nanoscale analysis. See, e.g., Georg H. H. etal., “Analysis of Detergent-Resistant Membranes in Arabidopsis. Evidencefor Plasma Membrane Lipid”, Plant Physiol. 2005 January; 137(1):104-116, incorporated by reference herein.

Chemical analysis is another example. A variety of tests can beperformed to, for example, identify a chemical trait of the tissue.

Other procedures or analyses are, of course, possible. The tissueremoval step provides a sample for such analyses. One skilled in the artis familiar with the different analyses and testing that can be done onseed.

5. Selection From Candidate Seed (Step 211)

Once analysis has been completed, results or information from theanalysis can be used to, for example, distinguish a seed from otherseed, or identify a trait of the seed. This can be used to select oneseed over another, or select a seed because of its trait. One example isa seed that, through genotyping, is indicated to be moredrought-resistant than other genotypes. By effective non-destructiveablation of a seed with a laser (or other removal of seed tissue), andby an appropriate genotyping assay, a seed indicative of droughtresistance genetic make-up can be identified.

As diagrammatically illustrated in FIG. 1, selection can be from aplurality of different candidate seed. The different candidate seed 1,2, . . . n are identified and collected (step 202). A first sample seed1 (step 203) is processed through steps 204, 205, and 206, and a resultof or data from the test of step 206 is recorded (step 207). One or moreother sample seed (e.g., sample(s) 2, 3, . . . n) are similarlyprocessed (steps 204-206) and the test results stored for each (207) incorrelation with their identifying information (202). This provides onebasis for comparison between two or more of the samples (step 210) andsubsequent selection between the two or more (step 211) of seed that isdeemed desirable (e.g., for further research or commercial production).As indicated in FIG. 1, the comparison between samples can be based onany of variety of factors capable of analysis with seed specific testsof the samples.

Importantly, non-destructive tissue removal and analysis allows suchidentification to be made without either planting the seed and waitingto test a tissue sample from its growing plant or having to use the landor greenhouse space, labor, and supplies to plant and grow the seed intoplants. The controlled, precise, non-destructive removal of seed tissuefor testing, or to gain access to relevant underlying tissue orstructure for testing, allows analysis to make selections based ontissue of the seed, not on a plant grown from the seed. As can beappreciated, this represents a potential substantial savings in time,labor, and resources, including land resources, for selection processesfor seed companies. The controlled, precise non-destructive tissueremoval is capable of substantial automation, thus improving through putand efficiency of plant selection processes.

With respect to corn seed, removal of at least exterior (pericarp)tissue is difficult. It was not considered practical or feasible to doso efficiently and/or non-destructively to the seed on a large scale.The pericarp 78 (FIGS. 5A and B) of corn seed is a relatively robustseed tissue (somewhat like a fingernail) and difficult to separate fromunderlying seed tissue structures. Any removal of a portion of thepericarp to expose tissue or structures inside the kernel is laboriousand difficult. This is well-known in the art. A variety of methods havebeen attempted to remove pericarp. Some include chemical baths(steeping) or mechanical methods (e.g., grinding). These require carefulworkers and are time consuming. They also tend to be destructive of theseed.

An important reason to expose interior tissues of a corn seed is to gainaccess to male and female genetic material to assay and evaluate geneticcontent. This allows researchers the ability to know if a seed containsa gene of interest. If so, the seed is then identified as a candidatefor further research or to produce commercial quantities of the seed.The method 200, controlled forces are used to remove specific seedtissue in a non-destructive manner. This, in turn, allows testing andanalysis, seed selection, and then planting and germination of theselected seed for further use. One further use is development ofcommercial quantities of seed from the selected seed; such as acommercial seed product for seed companies.

But additionally or alternatively, removal of tissue from a seedprovides a sample from the seed for testing. The method could be used toremove not only a portion of the pericarp but also a specific type andamount of interior tissue (e.g., endosperm or embryo). For example,controlled operation of a laser could ablate an area of the pericarp aswell as a portion of the embryo lying immediately under the pericarp.The debris from the ablation (i.e. the removed tissue) can be collectedand tested. The debris is essentially a sample of candidate seed. Thetesting of the debris is thus a testing of the seed. If controlledappropriately, the tissue could be removed by laser ablation in a mannernon-destructive of the remaining seed, so that the remaining seedretains germination potential. However, this is not required. By removalof a small sample from the candidate seed, the sample could beimmediately tested to allow rapid decisions to be made about the seedand its traits. Because the sampling and testing can be carried out on asingle seed (which is non-destructive of the plant or other seed of theplant), the method can be not only rapid but provide relatively highthroughput for plural candidate seed.

There are other beneficial applications for a methodology of processingseed to remove a certain relatively accurate amount of tissue from theseed. A variety of situations exist where removal of some portion of theseed is desired. The method described above utilizes steps tonon-destructively remove desired seed tissues. Other uses for seedtissue or exposed seed tissue are well known in the art.

D. Specific Example 1 (FIGS. 2-14)

FIGS. 2-14 illustrate one specific approach to the method of FIG. 1. Thetool or method of ablation to remove seed tissue is a laser. In thisspecific example, a specific seed holder is used for positioning acandidate seed relative to the laser.

FIG. 2 sets forth diagrammatically a block diagram illustration of asystem and apparatus 300 to practice method 200 of FIG. 1. Plural seedsamples 301A-N are prepared and provided for processing and analysis toa seed handling system 302. Seed handling system 302 presents thesamples 301 to a seed holder 305 which defines a testing location 320. Atissue removal tool 302 is controllable by positioner 304 to operate ona seed in the test position 320, specifically to remove a specifiedamount of seed tissue from a specified area of the seed. Once the tissueis removed, a seed specific test 306 is performed on the seed. Asindicated, in this example, the test is performed at the testinglocation, which is the same location as the tissue removal step. Thiscan save time and improve efficiency of throughput. Test results 307 arecollected and can be recorded in computer memory 308, for example.

Reference numbers 310-315 show the general flow path of these samplesand test results from the samples. Many of these functions can besubstantially automated. This allows multiple sample seed to beprocessed with minimal manual steps, which can increase accuracy andefficiency.

FIG. 3 illustrates a laser ablation system 10 that could be used as thetissue removal tool to practice the exemplary method 200 and exemplarysystem 300 of FIGS. 1 and 2.

1. Tissue Removal Tool

In the system 10 illustrated in FIG. 3, a laser 16 is the tissue removaltool. One example is a Firestar™ f201 Series, Model # FSF201SB,water-cooled sealed carbon dioxide (CO₂), 200 watt laser commerciallyavailable from Synrad, Inc. of Mukiteo, Wash. (USA). Laser 16 hastypical characteristics and adjustability (e.g., power or intensity).

A CO₂ type laser has proven efficiency, as well as reasonable cost andhigh power capability. It runs in the infrared wavelengths. It is widelyused for cutting and welding, but is also frequently used for surgicalprocedures because the water in most biological tissue absorbs the CO₂laser's frequency of the light. Other types of gas lasers could be used,as can other types of lasers (e.g., chemical, metal vapor, solid state(e.g., YAG) and semiconductor).

Laser 16 normally would include an optics package, such as beam deliverycomponents (see reference numeral 130 at FIG. 8), to focus and controlthe laser beam. Conventional auxiliary equipment, such as power supply,control circuit, and the like, would also be used. Such optics andaccessories are typically available from the laser vendor ormanufacturer, as they are from Synrad. With the FSF201SB laseridentified above, a beam delivery system is used that transfers the rawlaser beam from the sealed laser and focuses it at the location to cutthe seed (e.g., the testing location). An example of an optic system isa Haas Laser Technologies Inc. 1.25″ series beam delivery system with a5″ focal lens. Any of the typical types of laser cutting systems couldbe used, including flying optics, hybrid, and pivot-beam, to preciselycontrol movement of the laser beam relative to its target application.

By empirical testing and calibration, laser 16 can be set to ablate apattern or area of one side of a seed to a relatively controllabledepth. Following the manufacturer's set up instructions, laser 16 can beconfigured to produce laser beam 132 of a certain width, power,modulation, and color designed for desired ablation of a surface of acorn kernel to remove an area of pericarp and provide access to tissuesunderneath the pericarp, and to do so non-destructively.

It is to be understood that lasers can be controlled so accurately andminutely that it is possible, if desired, to etch a marking, letters, ornumbers on the surface of seed kernel, if desirable. One use would be tomark an identification of the seed sample directly on the seed.

For adequate control of position, size, and depth of tissue removal ofcorn seed, the tissue removal tool ideally should have a pre-determinedspatial resolution. The ablation can be varied across a seed. It couldbe varied from seed to seed across plate 18. It could be varied inamount (e.g., area and volume) of tissue removed, position of tissueremoved, or which tissue is removed (e.g., pericarp, endosperm, and/orembryo). If the objective is exposure to cells for genetic testing, thelaser ablation can open up the interior of specific tissue, parts, orstructures of the seed. In one example, the ablated seed can then beplaced into a solution (or a solution added to the well 40 in which aseed is ablated) to extract DNA, and then analyze it. The solution andDNA extraction methods are well-known to those skilled in the art.

It is to be understood that it may be possible that other forms ofenergy or forces could be used for the removal of tissue or structurefrom seed. Some examples have been mentioned previously.

In this example of laser ablation, set up and application of laserenergy as the mode of ablation is akin to laser ablation in medical,usually surgery, or biological applications. Seed is similar to humansoft tissue, inter alia, because it is biological and contains asignificant amount of water.

The process is greatly affected by the nature of the material and itsability to absorb energy. Therefore, the wavelength of the ablationlaser should have a minimum absorption depth. While these lasers canaverage a low power, they can offer peak intensity and fluence given by:

Intensity(W/cm²)=average power(W)/focal spot area(cm²)

Peak intensity(W/cm²)=peak power(W)/focal spot area(cm²)

Fluence(J/cm²)=laser pulse energy(J)/focal spot area(cm²)

while peak power is

Peak power(W)=pulse energy(J)/pulse duration(s).

Laser ablation of seed is similar to laser soft tissue surgery.Interaction of a highly focused laser light beam with soft tissuebasically vaporizes the soft tissue with high water content. Such alaser can make a very small incision. CO₂ laser wavelengths (e.g.,10,600 nm) are highly absorbed by water-containing biological tissues.They also tend to be less costly than solid state Er:YAG lasers, whichalso feature a wavelength that is highly absorbed by water.

Ablation of a seed is performed similarly to the surface ablation of thecornea for several types of eye refractive surgery (e.g., LASIK andLASEK). Material is removed from the solid by irradiating it with afocused laser beam. At low laser flux, the material is heated by theabsorbed laser energy and evaporates or sublimates. At high laser flux,the material is typically converted to plasma. Usually, laser ablationrefers to removing material with a pulsed laser, but it is possible toablate material with a continuous wave laser beam if the laser intensityis high enough.

The depth over which the laser energy is absorbed, and thus the amountof material removed by a single laser pulse, depends on the material'soptical properties and the laser wavelength. Laser pulses can vary overa very wide range of duration (millisecond to femtoseconds) and fluxes,and can be precisely controlled.

Types of laser setups can include, but are not limited to, movingmaterial, hybrid, and flying options systems. Moving material has astationary cutting head and moves the material under it. It requiresfewer optics, but requires moving the work piece or material beingablated. Hybrid lasers provide a table which moves in one axis and movesthe head along the shorter axis. Flying optics feature a stationarytable and a cutting head (with laser beam) that moves over the workpiece in both of the horizontal dimensions. Another example of beammovement is by a rotating or vibrating mirror. The mirror moves in amanner which may trace out the desired pattern on the surface.

The point where the laser touches the surface should be on the focalplane of the laser's optical system and is usually synonymous with itsfocal point. This point is typically small (e.g., less than a fractionof a millimeter depending on wavelength). Only the area inside thisfocal point is significantly affected when the laser beam passes overthe surface. The energy delivered by the laser changes the surface ofthe material under the focal point. It may heat up the surface andsubsequently vaporize the material, or perhaps the material may fracture(known as “glass” or “glass up”) and flake off the surface. This is howmaterial is removed.

Different patterns can be engraved on objects such as seed byprogramming a controller to traverse a particular pattern for the laserbeam over time. The trace of the beam is carefully regulated to achievea consistent removal depth of material. Criss-cross paths are avoided.The speed of beam movement is also considered. Changing the intensityand spread of the beam allows more flexibility. For example, by changingthe proportion of time (known as “duty-cycle”) of the laser is turned onduring each pulse, the power delivered to the surface can be controlledappropriately for the material.

As can be appreciated by those skilled in the art, the following arefactors in controlling laser operation:

(a) speed of motors moving the laser beam relative the seed;

(b) wattage of the laser (usually a defined amount, e.g., 75 watts),

(c) frequency of the laser (controls heat generated when the laser hitsthe seed).

Also, other operations can affect laser sampling. One would be use ofcompressed air (e.g., 30 psi) to remove debris from the area where thelaser is striking. Vacuum is an alternative.

Ventilation through blowers or a vacuum pump can be used to remove thefumes and smoke arising from this process, and for removal of debris onthe seed surface to allow the laser to continue essentially engravingthe material.

2. Seed Holder

Each seed can be held in position for tissue removal by the tissueremoval tool. One example is a container including a well or cavitydefined by a sidewall between a bottom and open top. FIGS. 3 and 4A-Dillustrate a multiple well container or plate 18 having a plurality(ninety six) of wells 40 arranged in an indexed matrix of rows andcolumns (eight rows A-H and twelve columns 1-12). Each well position canbe indexed by row/column (e.g., A/1, A/2, . . . H11, H12). In thismanner, identifying information about a seed in a well can be recordedrelative to the particular well in which it is placed to maintain acorrelation between each seed in plate 18 and its identity. Asillustrated in FIG. 4A, in this example wells 40 are equally spacedapart on top 42 of plate 18. The ninety-six wells 40 correspond with aconventional number of seed or samples used in plant breeding assays ormany laboratory tests.

Plate 18 can be of any of a variety of materials and configurations. Itsprimary functions are to hold each seed in a static position relative tothe tissue removal tool and in isolation from other seed so there is noco-mingling between seed.

One example of plate 18 has the following characteristics. It is solidmetal with machined wells 40 of cylindrical shape. Examples of metalinclude but are not limited to aluminum, steel, or brass, or alloysthereof. Others are possible. Alternatively, plastics could be used. Anexample of plastic is acrylic. Other materials are possible. Examplesare rubber or metal foil. The material should be compatible with thetissue removal tool and its forces.

An example of aluminum would be raw aluminum, 6061 grade. The sidewalland bottom of each well could be configured to absorb laser light,reduce reflections, and/or cause diffusive reflection of the laserlight, if a laser beam tissue removal tool is used. For metals or alloysof metal, those surfaces could be powder-coated, anodized, sandblasted,painted, or otherwise textured or configured to reduce reflections or besubstantially light diffusive.

In the example of plate 18, it is designed to contain a single seed perwell. Each well has a specific design element which aids in centeringthe seed in the well (e.g., conical bottom as discussed below). The wellis also powder coated with a substance which minimizes laser reflectionsor is light diffusive. An example is Alesta™ brand powder coating, fromDuPont of Wilmington, Del. USA. Sandblasting and anodization are othermethods of altering a surface, especially aluminum, to make it lessspecular and more diffusive. Other ways are possible.

For plastics, the material itself can be light absorbing or lightdiffusive, or a reflection-deterring texturing could be machined ormolded into the plastic. Another method of reducing reflections is toalter the geometry of the bottom and/or sidewall defining a well.Angling the surfaces of those portions can assist in deterring unwantedreflections of a laser beam out the open top of the well.

By using individual wells for each individual seed, singulation andisolation of each seed from other seed is automatically achieved. Eachwell 40 is a cylindrical bowl with a conical countersunk bottom 58.

Positioning and orientation of the seed can be accomplished in a varietyof ways. With respect to plate 18, each well 40 is made wider than thelongest dimension of a kernel 60 but has a conical, countersunk floor58. This assists in centering the corn seed 60 in well 40. The shape andinternal contents of a typical corn seed are illustrated by FIGS. 5A andB. Note how the embryo 74 is near the tip cap end 66 of the seed, andnear one flattened side face 62. The endosperm 76 occupies much of sideand end opposite the tip cap 62. It has been found that the conicalcountersink of floor or bottom 58 of well 40 helps automatically centera corn seed (or any seed or particle) in well 40. Also by appropriatediameter, well 40 and conical countersink tend to position a corn seedwith its flattened faces generally parallel to a plane across the bottomof well 40. This allows one of the largest surface area sides of thecorn seed to be exposed to the top of well 40. The laser can be set forany depth for each well (see plane D in FIG. 8). By initialization andempirical testing, an average depth for a particle set of seed samplescan be established. This avoids having to adjust the depth of cut foreach seed. It has been found to work well for most corn seed. However,depth of cut, as well as area of ablation can be controlled differentlyfor each seed sample, or they can be adjusted for different types ofseed, or different varieties of seed, if needed, as average seed sizecan vary. As can be appreciated, the laser can make multiple scansacross the same locations of the seed to incrementally remove tissueuntil a certain final depth. Alternatively, one scan is used to cut tothe final depth. Empirical testing can establish the desired process.

FIG. 6A illustrates an alternative example of a seed holder. A blisterpack type member 100 has a base sheet or substrate with multiple holesfrom which plastic bubble-shaped clear plastic containers 102 extend.Further detail can be found at U.S. patent application Ser. Nos.12/235,100, filed Sep. 26, 2007, and 12/545,283 filed Aug. 21, 2009,which applications are assigned to the owner of the present applicationand incorporated by reference herein in their entirety. Containers orbubbles 102 are analogous to wells 40 of plate 18. Each bubble wouldreceive, singulate, and isolate a seed from other seed. A release sheetcan be removably adhered or attached over the top of the holes insubstrate 100 to seal the contents of the bubbles 102, if desired. FIG.6A shows blister pack 100 configured to have an identical number andspacing of bubbles 102 relative to number and spacing of wells 40 ofplate 18. Blister pack 100 could be used to store candidate seed samplesin an indexed fashion (8 rows×12 columns) with a release sheet overbubbles 102. Those 96 samples could be easily transferred to the 96wells of plate 18 by removing the release sheet from blister pack 100,inverting plate 18 with empty wells over blister pack 100 with wells 40and bubbles 102 aligned, and then inverting both blister pack 100 andplate 18 to transfer seed from blister pack 100 to plate 18. But, analternative use of blister pack 100 could be as a substitute for plate18. Blister pack 100 can be placed with the holes facing up and withoutany release sheet over them. Individual seed kernels can be placed intoeach bubble. The tissue removal tool can then be manipulated, asdescribed with respect to plate 18, to move to and operate on a seed ina first bubble 102, then move to the next seed and bubble, and so on.

Other seed holders are possible. For example, a pedestal or pin with ahead adapted with a receiver or cradle might be used to hold a singleseed, isolated from other seed, in a manner that can be presented to andoperated upon by a tissue removing tool. Tubes in racks or press andseal containers are other examples of devices that can isolate and holdindividual seed in a position for tissue removal.

FIG. 18 illustrates an example of an alternative seed holder. In system150, a wheel 154 turns in synchronization with a seed filler device 152.Wheel 154 has multiple magnets 156A-F equally spaced apart around itsperimeter. Each seed 60 has been previously painted or dipped inmagnetic or iron-based paint 158. In synchronicity and generallyconcurrently, a seed 60B drops from seed filler 152. Prior dropped seed60C, bound to magnet 156C by magnetic attraction of iron-based paint 158to magnet 156C, rotates towards laser beam 132 of laser 16. Seed 60D isat the testing position and has tissue removed by laser beam 132.Processed seed 60E moves toward scraper 162. Seed 60F is knocked fromits magnet 156F by scraper 162. Thus, system 150 similarly singulatesand isolates single seed from one another, and uses a tissue removaltool. Furthermore, even though without a container such as a well orbubble, each seed is positioned rather uniformly. In fact, by placingthe magnetic paint 158 (e.g., magnetic primer paint commerciallyavailable from Rust-oleum of 11 Hawthorn Parkway, Vernon Hills, Ill.60061 USA, or magnetic wall paint from Kling Magnetics, PO Box 348 343Rt. 295-Chatham, N.Y. 12037 USA) in the same position on each seed 60(here on its crown), system 150 generally uniformly positions each seed.It can more uniformly and automatically orient each seed 60 in the samegeneral orientation to laser beam 132. Further details about a systemlike system 150 can be found in U.S. application Ser. No. 11/939,402,filed Nov. 13, 2007, which application is assigned to the owner of thepresent application and incorporated by reference herein. Theincorporated-by-reference application discloses utilization of a metalor ferromagnetic material applied to a portion of the exterior of aseed. The seed can then be automatically attracted to a magnetic field(of a permanent magnet or electromagnet). Depending on the position ofthe magnetic paint on the seed, the seed can automatically be positionedin a predetermined orientation. This would allow the combination to beused to position and hold a seed relative to a tissue removal tool.

System 150 can also use an automated seed filler or motion system tomove seed filler chute 110B in an orderly fashion so that seed 60, afterlaser processing, are placed in individual wells or bubbles in a tray orbubble pack 100B (see illustration of how seed 60A-F would end upserially deposited in row and column form). Alternatively, an automatedmotorized positioner or motion controller could move tray 100B relativeto chute 110B in such an orderly fashion.

Seed fillers or other similar seed or particle handling components thatcan be programmed and automated are available from a variety of vendorsincluding Elmor™ products from Elmor Angewandt Elektronik of Mangelegg58 CH-6430 Schwyz, Switzerland. Such machines can drop one seed at time,or fill multiwell containers serially, like a multiwell plate 18 or amulti-bubble blister or bubble pack. Other types of small particlehandlers or conveyors could be used to move, singulate, transfer, orotherwise handle individual seed. Another source for such machines arefillers and packagers, including for seed, from Visser InternationalTrade & Engineering B.V., P.O. box 5103, 3295 ZG 's-Gravendeel, TheNetherlands.

Although system 150 in FIG. 18 illustrates using a laser to cut off aclip or part of each seed, by appropriate setup and control, system 150could be used to ablate or remove just a small amount of surface tissue,as described with respect to system 10. This would likely require thatwheel 154 be stopped at least momentarily when a seed 60 is in the laserbeam path, and the laser beam 132 raster scanned across a side of seed60.

3. Automated Handling

Commercially available equipment can be used to automate orsemi-automate many of the functions of system 10. Examples are asfollows.

As indicated in FIG. 3, plate or other seed holder 18 can be positionedon base 12 in the field of movement of laser 16. In this example, plate18 contains ninety-six spaced apart wells 40 sized to each receive asingle corn kernel 60.

It has been found that processing of a plurality of seed (here 96) canbe done relatively rapidly in an automated fashion with system 10.However, since ablation of the seed is with laser energy, is not trivialas to how to present each seed to the laser beam. Similarly,complexities exist with other forces that might be used for tissueremoval (e.g., water jet, grinding).

A base 12 (platform, table, or the like) supports a frame 14 which inturn supports an automated tissue removal tool. In FIG. 3, the tool islaser 16 that is programmably movable via an XYZ positioner system 20 orother motorized positioning devices or systems.

Any of a variety of commercially available motorized positioners couldbe utilized. FIG. 3 diagrammatically illustrates that a moveable rail 22can move along the top of frame 14 by a computer-controlled motor 24. Acarriage 26 can move across rail 22 by computer controlled motor 28.Laser 16 can move up and down relative to the top surface of plate 18 oncarriage 30, which is computer controlled through motor 32. Carriage 30moves on an arm that is attached to carriage 26. As indicated in FIG. 3,this allows multiple degrees of freedom of movement of laser 16 relativeto plate 18. The ways in which the three dimensional movement of thetissue removal tool occurs relative to the seed holder can vary. It ispossible that the seed holder could be moved relative to the laser, orboth moved relative to each other.

A controller 36, such as are commercially available, can be incommunication with a computer 38. Computer 38 includes software thatallows the user to program movement of XYZ positioner 20, and thus laser16, relative to each well 40 in plate 18. Controller 36 would execute onthat program through some sort of power supply in junction box 34 thatwould control motors 24, 28, and 32 to very accurately position laser 16and its beam 32, and move the beam across a seed. In this way, anautomated laser ablation of a single seed in each well 40 of the 96 welltray 18 can be accomplished without manual labor or control.

Examples of positioner systems with programmable control are availablefrom Synrad and made by such companies as Techno Inc. of New Hyde Park,N.Y. USA; Anorad Corp. of Shirley, N.Y. USA; and Aerotech, Inc. ofPittsburgh, Pa. USA.

Examples of other automation would include a seed filler, as previouslydiscussed. It could be used to move a single seed and drop it in aspecified well, bubble, or designated location of a seed holder.

Furthermore, equipment can be used to move seed from a well, bubble orother location to a designated location after the tissue has beenremoved. An example would be to utilize magnetic tape or other magneticcoating or attachment to each seed 60, as described above with respectto FIG. 18 to allow automated movement of each seed between locations.An electromagnet or other magnetized subject could be used to pick upindividual seed 60 from a batch of seed 60, move those individualizedseed into position over individual wells 40, and then deposit them inwells 40. By reverse process, after ablation, the system could grab theseed out of each well and move them to another station. A still furtheralternative would be vacuum systems, such as can be developed with theskill of the ordinary artisan, and could be used to pull seed from abatch, singulate them, deposit them in wells 40, and then remove them atan appropriate time.

Further, the seed holders such as plate 18 or blister pack 100, or otherseed holders that have a well or cavity, could be used for additionalfunctions over and above singulating, isolating, and holding a seed foroperation by a tissue removal tool. Well 40, bubble 102, or the likecould also function as an assay vessel. One example is that a liquidmixture for polymerase chain reaction (PCR) could be placed directlyinto well 40 or bubble 102 after tissue removal. The reaction couldoccur and be analyzed for any of a wide variety of data such as is wellknown by those skilled in the art. This avoids having to move and keeptrack of identification of multiple seed. Such in situ seed specificanalysis can occur efficiently and with relatively high throughput ofmultiple samples. Results of the analysis can be recorded (e.g., in adatabase or otherwise) with correlation to the identity of each seed.Those results can then be used in a number of ways.

Automated liquid handling equipment could also be used to move liquid orliquid mixtures or suspensions in a controlled, preprogrammed manner. Anexample is the liquid PCR assay described above. Liquid may be used, forexample, for other testing of the seed after tissue removal. Such liquidhandling equipment is commercially available and widely used inlaboratory settings. Examples are automated liquid handling systems fromPerkinElmer Life And Analytical Sciences, Inc., 940 Winter Street,Waltham, Mass. 02451 USA.

As indicated in FIG. 3, a computer 38 can be used to not only facilitateprogramming of the automated handling equipment, but also can be used torecord and store information about the tissue removal and/or any seedspecific analysis performed on the seed.

Other handling components could include a sub-system for keeping trackof identity of the samples or sets of samples. Bar codes or othermachine-readable labels or tags (e.g., RF tags) could be mounted on anyof the containers, carriers, trays, or plates that include seed. Thiswould allow maintenance of correlation of samples to originalidentifying information.

4. Operation

For efficient, high throughput operation of system 10 of FIG. 3,individual kernels 60 are deposited in each well 40 of plate 18. FIG. 6Aillustrates one possible way to do so. A blister pack 100, having 96clear plastic bubbles 102, can contain seed of known origin or identity.A peel-off adhesive cover (not shown) can contain the seed in each ofthe bubbles 102, even when blister pack 100 is inverted. Blister pack100 can be brought to ablation plate 18, the peel off cover removed, andplate 18 inverted and placed so that each of wells 40 is in alignmentwith a bubble 102. The combination of bubble pack 100 and plate 18 canbe turned over and each of the 96 seed from bubble pack 100 would fallinto a corresponding well 40 and plate 18. Plate 18 could then be placedin a referenced position on base 12. After ablation, the reverseprocedure could be used to place seed back into the bubbles 102 ofbubble pack 100 for transportation to a next step if desired.

FIG. 6B shows an alternative system. A seed tube 110 could be incommunication with a seed singulator 112. The combination could delivera single seed down tube 110 that could be aligned with a well 40. Tube110 could be moved to the next well 40 and the next single seeddelivered, and so on. Tray or seed fillers are commercially available.Examples have been given earlier.

There are other ways to place seed in wells 40. One is simply tomanually place a seed in each well 40. This may be preferable in thatthe user can ensure that the seed is centered in well 40 and that a flatwide side of the corn kernel is basically facing up relative to the opentop into well 40. As previously mentioned, plate 18 can be intentionallymanufactured to have a conical bottom 58 for each well 40 to assist incentering kernel 60 in well 40, as the geometry of such a wellencourages the corn seed to lie in a manner where a wide, flat side isfacing up.

Once a single seed 60 is in each well 40, and plate 18 is in itsreference position on base 12 of system 10, controller 36 would beginthe ablation process with laser 16 to remove specific tissue from theseed.

As is illustrated in FIG. 7, controller 36 could include software on PC38 which allows the user to design the specific ablation pattern foreach well 40. A computer display 124 on PC 38 could show the center ofeach well 40. The user could designate or design the specific ablationpattern in relation to well 40. As shown in FIG. 7, the pattern can berectangular in the horizontal plane (see reference numeral 122). Thedimensions of rectangular pattern 122 can be selected and can even bedisplayed on computer screen 124. The user could also select powerlevel, color, modulation, and other relevant operational parameters tocontrol how that rectangular shape is ablated, cut, etched, or otherwiseformed in each seed, as well as the depth.

As can be appreciated, a wide variety of patterns are possible withlaser 16. FIGS. 8A and B and 9A-C illustrate one example of a possibleshape.

In this example, laser 16 is configured with optics 130 to create alaser beam 132 that has a 0.0005 cutting width (at ¼ inch focal length).The dimension of shape 122 is 0.2 inch square. As illustrated in FIG.8B, controller 36 is programmed so that laser beam 132 scans back andforth on the surface of kernel 60 to ablate or remove tissue to makethat shape. As indicated in FIG. 8B, the beam would cut a first swath92A of 0.0005 from one side of shape 122 to the other. It would then goback along a slightly different path (reference number 96B). It wouldscan back and forth progressively etching or ablating additionalmaterial but keeping the rectangular shape 122 until a final depth isreached. FIG. 8B illustrates linear paths 92A through 92H. In practice,there would be on the order of 30 to 40 scans to complete the cuttingout of cavity 80 in the programmed shape 122 of FIG. 7.

In this example, just enough tissue is ablated to expose underlyingrelevant tissue or structure in the corn kernel. By scanning the laserbeam in a relatively rapid manner, ablation of the seed tissue isaccomplished without excessive heating or other conditions whichmaterially adversely affect germination viability. Automated system 10could allow ninety six different seed to be sequentially ablated in thismanner without any manual human steps.

FIG. 8A illustrates diagrammatically and not to scale the cavity 80 of arectangular prism shape. Laser ablates material from seed 60 in thatshape to remove the outer pericarp and expose interior tissues. Thiscould be endosperm. It could be the embryo. In any case, the process canbe configured to not materially affect viability for germination of cornseed 60. FIGS. 9B and 9C show alternative views of cavity 80 created bylaser 16 for that seed.

It is to be understood that the exact manner in which laser 16 createscavity 80 can vary. Beam 132 can be moved back and forth with an XYZpositioner such as indicated in FIG. 1. Alternatively, there could beoptical methods to change the angle of beam 132 or create back and forthscanning cutting action of the beam.

Once laser ablation of a seed 60 in well 40 at the reference A1 positionof plate 18 (see FIG. 4A) is completed, laser 16 would be moved bycontroller 36 to a referenced position over well 40 at position A2 ofplate 18 and the laser ablation process to etch shape 122 for that welland seed would be conducted. Once completed, laser 16 would move toposition A3 and so on until completion of row 1. It would then begin onthe next row and continue until all 96 positions were completed.

It can be appreciated that the goal is usually to remove enough materialto gain reasonable access to a specific interior tissue(s) of seed 60.For these purposes it is not essential that the area ablated isabsolutely centered on a side of seed 60 or that it be precisely to acertain depth. By empirical testing and adjustment, and relativeconsistent positioning of a seed 60 in each well 40 (that is, asconsistent as possible positioning in the center of the well 40),programming the laser to cut a shape 122 centered with the center ofwell 40 usually results in ablation of enough material to gainreasonable exposure to the desired interior tissues.

Programming of the shapes 122 is non-complex in many systems. Commercialsystems usually allow the shape to be selected and displayed in a printfile which is then communicated to the controller 36. An appropriatetemplate or graphic user interface (GUI) at PC 38 or controller 36allows adjustment of shape, area, and depth of cavity 40.

FIGS. 10A-C through FIGS. 14A-C are included just to give a fewadditional examples of how the shapes and depths of the ablation can bevaried. As illustrated in FIGS. 10A-C, a first larger rectangular prismcavity near the top of the surface of seed 60 could be created to afirst depth. A smaller area rectangular prism shape could then be etchedto a lower depth. A third, still smaller rectangular prism could beetched to a still lower depth. This creates a stair step type cavity80B. FIGS. 11A-C show that two rectangular channels could be etched inthe seed, a smaller spaced apart from and inside a larger one. FIGS.12A-C illustrate removal of a rectangular area over the embryo. FIGS.13A-C and 14A-C show the patterns could be other than rectangular, e.g.,more circular. More complex shapes are, of course, possible.

The high flexibility of the laser beam can make an almost unlimitednumber of shapes and depths of cavities. These shapes also can bedesigned to non-destructively remove tissue to expose underlying seedtissue of interest. Because the laser can have such a relatively narrowbeam width, the system allows very accurate and minute positioning ofthe beam relative to the particle or item being ablated. Raster scanningof the beam allows progressive and precise control of final depth ofcut. Optionally, the beam can be directed to a very specific portion ofthe item or seed. For example, laser ablation could be programmed forcorn kernels to remove tissue just at or near the tip cap at one end orjust near the other end or somewhere in between. Vector-based laser beamcontrol is also possible. Vector-based movement follows the line andcurve of a pattern.

Once all 96 seed have been ablated, they are ready for tests, asdesired, to obtain information about the seed. For example, a variety ofgenetic testing procedures or assays could be used to identify thegenetic material present in the seed. By that direct testing of a seed,a plant researcher could thus make a rapid determination if the seed isdesirable for continued use in a plant advancement or breedingexperiment, or for commercial production.

Removal of specific portion(s) of seed tissue(s), or use of exposedportions of the remaining seed portion(s), can be utilized for specificlaboratory assays, which may include direct DNA, RNA, lipid, or proteinisolations. Thus, this embodiment can be utilized in plant breedingprocesses in which identification of seed with desired traits orcharacteristics for subsequent germination to maturity in the field ofgreen house can be relatively rapidly acquired directly from the seed.Examples of genetic analysis testing are set forth in U.S. Pat. Nos.6,472,185, and 6,368,806 which are incorporated by reference herein.

As is well-known in the art, the identity of each seed, as well as itshistory, can be known and maintained throughout this process by avariety of techniques. For example, in the blister pack example, FIG.6A, a bar code 108 or other machine readable label could be applied toblister pack 100 which identifies the origin and essential informationabout the seed in the blister pack on a well-by-well basis using the rowand column indexing letters/numbers. By maintaining each seed in itscorresponding column and row position in the blister pack, in plate 18,and back into blister pack 100 or into some other 96 well tray, theidentity of each seed can be maintained. This would allow seedidentified with the gene of interest to be known and their identitymaintained by recording the position in the 96 positions of the array.

E. Specific Example 2 (FIGS. 15-17)

Instead of, or in some cases in addition to, removing tissue to gainaccess to the interior of a candidate seed, the removed tissue (or aportion thereof) can be collected and tested or analyzed. The test(s) oranalysis(es) could be used to make selection decisions.

FIG. 15 shows in diagrammatic form a specific example. It is similar toFIG. 1 but with the following major differences.

The method 400 of FIG. 15 utilizes some tissue removal tool or method402 to remove specific tissue from a candidate seed 401A. Seed 401A canbe positioned in some holder component or position 405. The removedtissue (or a portion thereof) is collected in a collection container403. Seed specific analysis is conducted of the collected removed tissue(reference number 406. The results are used (step 407) to make decisions(e.g., selection or not of the type of seed 401A for further use).Optionally, the test results and/or decision(s) can be stored or used bya computer 408.

It is to be understood that either Example 1 or 2 could be at leastpartially automated. But also, either Example could lend itself torapid, local sample collection and analysis. For instance, a portablelaser assembly could be taken to an experimental growing plot. Candidateseed from a growing corn plant could be removed, placed in a single well40 and laser ablated. An appropriate solution could be added to theablated seed in the well 40, DNA extracted into the solution, and thesolution removed and genetically or otherwise evaluated. Or, the tissueremoved by laser ablation could be placed in an appropriate solution orother assay and genetically otherwise evaluated. The evaluations couldbe used to make growing site decisions about the plant from which thecandidate seed was taken. This avoids taking samples back to a remotelaboratory and the overhead of transport and keeping track of whichplant associates with which seed.

FIGS. 16 and 17 illustrate one example of how tissue removed from acandidate seed can be collected for analysis. Seed 70 is ablated by alaser 16 such as discussed in Example 1. A plume of fines or smallparticles (which act like smoke in the sense that they tend to float inthe air) created by laser ablation would separate from seed 60.Sometimes they reformulate and coat the sides of well 40. This requirescleaning of plate 18 after each ablation process. A vacuum hood or head140 (e.g., clear plastic) could be mounted on the optics or laser 16. Itcould be lowered with laser 16 over a well 40 during ablation of seed 60in well 40. By utilizing vacuum hood 140 in operative communicationthrough vacuum tube 144 to vacuum 142, those fines can be substantially,if not all, removed to eliminate this issue.

Alternatively, collection of the fine particles via vacuum or otherwise,can result in collection of enough material for testing, instead oftesting the seed. This would require that the laser ablate tissue ofinterest for the test. For example, if just pericarp is desired fortesting, the laser could be controlled to just ablate pericarp. Theremoved pericarp particles could be collected by vacuum and then tested.On the other hand, if endosperm was desired for testing, the laser couldablate the pericarp, the removed pericarp particles could be ignored orremoved, and then the laser could ablate exposed endosperm, which couldbe collected into a container by, e.g., vacuum. Embryo tissue could becollected by removing pericarp over the embryo, then laser ablating theexposed embryo and vacuum-collecting the embryo particles.

FIG. 16 illustrates in simplified form laser ablation and vacuumcollection from a single candidate seed. A seal or gasket 141 would sealhood 140 to the surface surrounding well 40 holding seed 70. Laser 16would be operated to cause laser beam 132 to ablate seed 70. Vacuumsource 142 (e.g., a vacuum pump) would be operated to cause fineparticles to move from well 40 into container 146, but leave seed 70 inplace. Container 146 could be removed and the collected particles fromseed 70 tested.

Examples of vacuum systems include a variety of commercially-availableparticle filtration systems or fume handlers that could remove and/orcollect the fines or collect. Particle extraction equipment iscommercially available from companies such as AER of Old Saybrook, Conn.USA and Fumex of Kennesaw, Va. USA. This equipment is typically used inindustrial air filtration/air pollution control systems for mist, dust,smoke, fume & gas/vapor contaminants in individual or combined forms.The system can include cartridge and bag dust/fume collectors, wet dustcollectors, electrostatic precipitators, media filtration systems, andother components.

FIG. 17 illustrates that a tray with multiple wells 40 could be usedwith the vacuum extraction laser ablation system of FIG. 16. This wouldlend itself to efficient vacuum collection of removed ablated tissuefrom a plurality of candidate seed.

An alternative to vacuum collection would be to add a gel substance toeach well 40. The gel would be transmissive of the laser beam. Finesresulting from laser ablation would tend to be collected by andsuspended in the gel. The laser may have to be adjusted (which could beaccomplished by empirical testing) to use a deeper cutting power if gelis used. It is possible that the fines collected in the gel could beextracted, collected, and assayed. To generate sufficient quantities offines for some tests, the laser or other tissue removal tool may have toremove more tissue than if just removing enough to expose interiortissue.

F. Options and Alternatives

It will be appreciated that the present invention can take many formsand embodiments. The embodiments described in detail herein are by wayof example only and not by limitation. Variations obvious to thoseskilled in the art would be included within the invention. However, afew additional examples of options, alternatives and variations, areprovided below.

1. Types of Seed

The system and method described above can be applied to seed other thancorn seed in analogous ways. Adjustments may be needed, as are withinthe skill of those skilled in the art.

2. Types of Tissue Removal Tools

As discussed previously, tissue removal from candidate seed can beaccomplished by different methods or components (collectively referredto as “tools”). A laser is one such tool. It can be used in one mode tocreate small particles. In another mode is can be used to cut off apiece of a seed (see, e.g., FIG. 18 and associated description of asimilar configuration shown and described in application Ser. No.11/939,402, filed Nov. 13, 2007, which application is assigned to theowner of the present application and incorporated by reference herein inits entirety.

Other tissue removal tools have been mentioned previously. applicationSer. No. 11/939,402 includes additional details and examples.

3. Types of Analysis on the Seed

Various assays can be performed on the seed. Some examples have beengiven previously. One example is that an assay solution could be placeddirectly in wells 40 after seed 60 are ablated or tissue removed orexposed. The solution can be extracted and tests run to identify geneticmaterial of interest. The wells can be drained and the seed moved to acarrier or package in preparation for further use. Alternatively, seedidentified as having a gene of interest could be removed from theircorrelated position in the array of plate 18 and the remaining seeddiscarded. Another alternative is, after ablation, to move seed 60 toanother container where an assay could be conducted. Additional types oftesting can include, but is not limited to, genetic, physical, orchemical analysis on a cellular, molecular, or nanoscale level. Somenon-limiting examples are:

-   -   a. Spectroscopic;    -   b. Genetic;    -   c. Various nucleotide extractions and fingerprinting (e.g., DNA,        RNA isolation);    -   d. Protein and lipids isolation;    -   e. Phenotyping;    -   f. Trait or characteristic identification;    -   g. Genetic marker assisted identification and selection;    -   h. High throughput screening.

Those skilled in the art are familiar with the types of analyses thatcan be conducted on biological tissue, and which may be desirable orneeded in making research and development decisions, as well ascommercial production decisions, for seed.

A few examples of genetic analysis tests are as follows. Markerscorresponding to genetic polymorphisms between members of a populationcan be detected by methods well established in the art. These include,e.g., PCR-based sequence specific amplification methods, detection ofrestriction fragment length polymorphisms (RFLP), detection of isozymemarkers, detection of allele specific hybridization (ASH), detection ofamplified variable sequences of the plant genome, detection ofself-sustained sequence replication, detection of simple sequencerepeats (SSRs), detection of single nucleotide polymorphisms (SNPs), ordetection of amplified fragment length polymorphisms (AFLPs). Othersexist. Varieties of analysis for physical or chemical traits also existand can be used.

Just a few methods of seed or seed tissue analysis have been mentioned.Others are known to those skilled in the art. A sample portion of a seedcan be analyzed, or the remainder of the seed from which the sample istaken. The sample can be a single piece or multiple pieces. It can evenbe plural small particles. An example is what might be called debristhat is generated, for example, when laser ablating a seed. Asdiscussed, the debris scatters in small particles and can be like aplume of dust or smoke. It can be collected for analysis. Real-timefluorescence analysis is an example to detect the presence of certaingenes. Another example of collection of seed debris from laser ablationis to use a tape with adhesive side above and facing the seed. The lasercould pass through or around the tape, ablate the seed, and cause aplume of debris to rise. The debris would stick to the tape. Real-timefluorescence analysis could be used to analyze the debris on the tape.

Another option is to analyze the seed which has been ablated. Forexample, laser ablation could remove debris to leave a seed with acavity (see, e.g., FIGS. 12A-C). An appropriate solution could be addedto cavity to exact genetic material from the seed into a solution. Thesolution could be analyzed, e.g., for an indication of the presence of agene or genes.

a. Types of Application of Analysis of the Seed

Examples of applications of the tests include but are not limited tosuch things as

-   -   a. Plant breeding processes for traits or characteristics;    -   b. DNA or non-DNA identification;    -   c. Identification of seed with desired traits or characteristics        for subsequent germination to maturity in a field or green        house;    -   d. Selection based on presence or absence of desired trait;    -   e. Selection based on presence or absence of genetic marker.

Use of information from testing seed is set forth in U.S. Pat. No.7,227,065, incorporated by reference herein. Examples are as follows.

In addition to phenotypic observations, the genotype of a plant can alsobe examined. A plant's genotype can be used to identify plants of thesame variety or a related variety. For example, the genotype can be usedto determine the pedigree of a plant. There are many laboratory-basedtechniques available for the analysis, comparison and characterizationof plant genotype; among these are Isozyme Electrophoresis, RestrictionFragment Length Polymorphisms (RFLPs), Randomly Amplified PolymorphicDNAs (RAPDs), Arbitrarily Primed Polymerase Chain Reaction (AP-PCR), DNAAmplification Fingerprinting (DAF), Sequence Characterized AmplifiedRegions (SCARs), Amplified Fragment Length Polymorphisms (AFLPs), SimpleSequence Repeats (SSRs) which are also referred to as Microsatellites,and Single Nucleotide Polymorphisms (SNPs).

Isozyme Electrophoresis and RFLPs as discussed in Lee, M., “Inbred Linesof Maize and Their Molecular Markers,” The Maize Handbook,(Springer-Verlag, New York, Inc. 1994, at 423-432) incorporated hereinby reference, have been widely used to determine genetic composition.Isozyme Electrophoresis has a relatively low number of available markersand a low number of allelic variants. RFLPs allow more discriminationbecause they have a higher degree of allelic variation in maize and alarger number of markers can be found. Both of these methods have beeneclipsed by SSRs as discussed in Smith et al., “An evaluation of theutility of SSR loci as molecular markers in maize (Zea mays L.):comparisons with data from RFLPs and pedigree”, Theoretical and AppliedGenetics (1997) vol. 95 at 163-173 and by Pejic et al., “Comparativeanalysis of genetic similarity among maize inbreds detected by RFLPs,RAPDs, SSRs, and AFLPs,” Theoretical and Applied Genetics (1998) at1248-1255 incorporated herein by reference. SSR technology is moreefficient and practical to use than RFLPs; more marker loci can beroutinely used and more alleles per marker locus can be found using SSRsin comparison to RFLPs. Single Nucleotide Polymorphisms may also be usedto identify the unique genetic composition of the invention and progenylines retaining that unique genetic composition. Various molecularmarker techniques may be used in combination to enhance overallresolution.

Maize DNA molecular marker linkage maps have been rapidly constructedand widely implemented in genetic studies. One such study is describedin Boppenmaier, et al., “Comparisons among strains of inbreds forRFLPs”, Maize Genetics Cooperative Newsletter, 65:1991, pg. 90, isincorporated herein by reference.

Molecular markers, which includes markers identified through the use oftechniques such as Isozyme Electrophoresis, Restriction Fragment LengthPolymorphisms (RFLPs), Randomly Amplified Polymorphic DNAs (RAPDs),Arbitrarily Primed Polymerase Chain Reaction (AP-PCR), DNA AmplificationFingerprinting (DAF), Sequence Characterized Amplified Regions (SCARs),Amplified Fragment Length Polymorphisms (AFLPs), Single NucleotidePolymorphisms (SNPs) and Simple Sequence Repeats (SSRs) may be used inplant breeding methods.

One use of molecular markers is Quantitative Trait Loci (QTL) mapping.QTL mapping is the use of markers, which are known to be closely linkedto alleles that have measurable effects on a quantitative trait.Selection in the breeding process is based upon the accumulation ofmarkers linked to the positive effecting alleles and/or the eliminationof the markers linked to the negative effecting alleles from the plant'sgenome.

Molecular markers can also be used during the breeding process for theselection of qualitative traits. For example, markers closely linked toalleles or markers containing sequences within the actual alleles ofinterest can be used to select plants that contain the alleles ofinterest during a backcrossing breeding program. The markers can also beused to select for the genome of the recurrent parent and against themarkers of the donor parent. Using this procedure can minimize theamount of genome from the donor parent that remains in the selectedplants. It can also be used to reduce the number of crosses back to therecurrent parent needed in a backcrossing program. The use of molecularmarkers in the selection process is often called Genetic Marker EnhancedSelection.

The goal of plant breeding is to combine, in a single variety or hybrid,various desirable traits. For field crops, these traits may includeresistance to diseases and insects, resistance to heat and drought,reducing the time to crop maturity, greater yield, and better agronomicquality. With mechanical harvesting of many crops, uniformity of plantcharacteristics such as germination, stand establishment, growth rate,maturity, and plant and ear height is important. Traditional plantbreeding is an important tool in developing new and improved commercialcrops.

Field crops are bred through techniques that take advantage of theplant's method of pollination. A plant is self-pollinated if pollen fromone flower is transferred to the same or another flower of the sameplant. A plant is sib pollinated when individuals within the same familyor line are used for pollination. A plant is cross-pollinated if thepollen comes from a flower on a different plant from a different familyor line. The term “cross pollination” and “out-cross” as used herein donot include self pollination or sib pollination.

Plants that have been self-pollinated and selected for type for manygenerations become homozygous at almost all gene loci and produce auniform population of true breeding progeny. A cross between twodifferent homozygous lines produces a uniform population of hybridplants that may be heterozygous for many gene loci. A cross of twoplants each heterozygous at a number of gene loci will produce apopulation of heterogeneous plants that differ genetically and will notbe uniform.

Maize (Zea mays L.), often referred to as corn in the United States, canbe bred by both self-pollination and cross-pollination techniques. Maizehas separate male and female flowers on the same plant, located on thetassel and the ear, respectively. Natural pollination occurs in maizewhen wind blows pollen from the tassels to the silks that protrude fromthe tops of the ears.

The development of a hybrid maize variety in a maize plant breedingprogram involves three steps: (1) the selection of plants from variousgermplasm pools for initial breeding crosses; (2) the selfing of theselected plants from the breeding crosses for several generations toproduce a series of inbred lines, which, individually breed true and arehighly uniform; and (3) crossing a selected inbred line with anunrelated inbred line to produce the hybrid progeny (F1). After asufficient amount of inbreeding successive filial generations willmerely serve to increase seed of the developed inbred. Preferably, aninbred line should comprise homozygous alleles at about 95% or more ofits loci.

During the inbreeding process in maize, the vigor of the linesdecreases. Vigor is restored when two different inbred lines are crossedto produce the hybrid progeny (F1). An important consequence of thehomozygosity and homogeneity of the inbred lines is that the hybridbetween a defined pair of inbreds may be reproduced indefinitely as longas the homogeneity of the inbred parents is maintained. Once the inbredsthat create a superior hybrid have been identified, a continual supplyof the hybrid seed can be produced using these inbred parents and thehybrid corn plants can then be generated from this hybrid seed supply.

An inbred line may be used to produce a single cross hybrid, a doublecross hybrid, or a three-way hybrid. A single cross hybrid is producedwhen two inbred lines are crossed to produce the F1 progeny. A doublecross hybrid is produced from four inbred lines crossed in pairs (A×Band C×D) and then the two F1 hybrids are crossed again (A×B)×(C×D). Athree-way cross hybrid is produced from three inbred lines where two ofthe inbred lines are crossed (A×B) and then the resulting F1 hybrid iscrossed with the third inbred (A×B)×C. In each case, pericarp tissuefrom the female parent will be a part of and protect the hybrid seed.

Large scale commercial maize hybrid production, as it is practicedtoday, requires the use of some form of male sterility system whichcontrols or inactivates male fertility. A reliable method of controllingmale fertility in plants also offers the opportunity for improved plantbreeding. This is especially true for development of maize hybrids,which relies upon some sort of male sterility system. There are severalways in which a maize plant can be manipulated so that is male sterile.These include use of manual or mechanical emasculation (or detasseling),cytoplasmic genetic male sterility, nuclear genetic male sterility,gametocides and the like.

Hybrid maize seed is often produced by a male sterility systemincorporating manual or mechanical detasseling. Alternate strips of twoinbred varieties of maize are planted in a field, and the pollen-bearingtassels are removed from one of the inbreds (female) prior to pollenshed. Providing that there is sufficient isolation from sources offoreign maize pollen, the ears of the detasseled inbred will befertilized only from the other inbred (male), and the resulting seed istherefore hybrid and will form hybrid plants.

The laborious detasseling process can be avoided by using cytoplasmicmale-sterile (CMS) inbreds. Plants of a CMS inbred are male sterile as aresult of genetic factors in the cytoplasm, as opposed to the nucleus,and so nuclear linked genes are not transferred during backcrossing.Thus, this characteristic is inherited exclusively through the femaleparent in maize plants, since only the female provides cytoplasm to thefertilized seed. CMS plants are fertilized with pollen from anotherinbred that is not male-sterile. Pollen from the second inbred may ormay not contribute genes that make the hybrid plants male-fertile, andeither option may be preferred depending on the intended use of thehybrid. The same hybrid seed, a portion produced from detasseled fertilemaize and a portion produced using the CMS system can be blended toinsure that adequate pollen loads are available for fertilization whenthe hybrid plants are grown. CMS systems have been successfully usedsince the 1950's, and the male sterility trait is routinely backcrossedinto inbred lines. See Wych, p. 585-586, 1998.

There are several methods of conferring genetic male sterilityavailable, such as multiple mutant genes at separate locations withinthe genome that confer male sterility, as disclosed in U.S. Pat. Nos.4,654,465 and 4,727,219 to Brar et al. and chromosomal translocations asdescribed by Patterson in U.S. Pat. Nos. 3,861,709 and 3,710,511. Theseand all patents referred to are incorporated by reference. In additionto these methods, Albertsen et al., of Pioneer Hi-Bred, U.S. Pat. No.5,432,068, describe a system of nuclear male sterility which includes:identifying a gene which is critical to male fertility; silencing thisnative gene which is critical to male fertility; removing the nativepromoter from the essential male fertility gene and replacing it with aninducible promoter; inserting this genetically engineered gene back intothe plant; and thus creating a plant that is male sterile because theinducible promoter is not “on” resulting in the male fertility gene notbeing transcribed. Fertility is restored by inducing, or turning “on”,the promoter, which in turn allows the gene that confers male fertilityto be transcribed.

These and the other methods of conferring genetic male sterility in theart, each possess their own benefits and drawbacks. Some other methodsuse a variety of approaches such as delivering into the plant a geneencoding a cytotoxic substance associated with a male tissue specificpromoter or an antisense system in which a gene critical to fertility isidentified and an antisense to that gene is inserted in the plant (seeFabinjanski, et al. EPO 89/3010153.8 Publication No. 329,308 and PCTApplication PCT/CA90/00037 published as WO 90/08828).

Another system useful in controlling male sterility makes use ofgametocides. Gametocides are not a genetic system, but rather a topicalapplication of chemicals. These chemicals affect cells that are criticalto male fertility. The application of these chemicals affects fertilityin the plants only for the growing season in which the gametocide isapplied (see Carlson, Glenn R., U.S. Pat. No. 4,936,904). Application ofthe gametocide, timing of the application and genotype specificity oftenlimit the usefulness of the approach and it is not appropriate in allsituations.

The use of male sterile inbreds is but one factor in the production ofmaize hybrids. The development of maize hybrids in a maize plantbreeding program requires, in general, the development of homozygousinbred lines, the crossing of these lines, and the evaluation of thecrosses. Maize plant breeding programs combine the genetic backgroundsfrom two or more inbred lines or various other germplasm sources intobreeding populations from which new inbred lines are developed byselfing and selection of desired phenotypes. Hybrids also can be used asa source of plant breeding material or as source populations from whichto develop or derive new maize lines. Plant breeding techniques known inthe art and used in a maize plant breeding program include, but are notlimited to, recurrent selection, mass selection, bulk selection,backcrossing, making double haploids, pedigree breeding, openpollination breeding, restriction fragment length polymorphism enhancedselection, genetic marker enhanced selection, and transformation. Oftencombinations of these techniques are used. The inbred lines derived fromhybrids can be developed using plant breeding techniques as describedabove. New inbreds are crossed with other inbred lines and the hybridsfrom these crosses are evaluated to determine which of those havecommercial potential. The oldest and most traditional method of analysisis the observation of phenotypic traits but genotypic analysis may alsobe used. Descriptions of breeding methods can also be found in one ofseveral reference books (e.g., Allard, Principles of Plant Breeding,1960; Simmonds, Principles of Crop Improvement, 1979; Fehr, “BreedingMethods for Cultivar Development”, Production and Uses, 2 ed., Wilcoxeditor, 1987).

Backcrossing can be used to improve inbred lines and a hybrid which ismade using those inbreds. Backcrossing can be used to transfer aspecific desirable trait from one line, the donor parent, to an inbredcalled the recurrent parent which has overall good agronomiccharacteristics yet that lacks the desirable trait. This transfer of thedesirable trait into an inbred with overall good agronomiccharacteristics can be accomplished by first crossing a recurrent parentto a donor parent (non-recurrent parent). The progeny of this cross isthen mated back to the recurrent parent followed by selection in theresultant progeny for the desired trait to be transferred from thenon-recurrent parent. Typically after four or more backcross generationswith selection for the desired trait, the progeny will containessentially all genes of the recurrent parent except for the genescontrolling the desired trait. But the number of backcross generationscan be less if molecular markers are used during the selection or elitegermplasm is used as the donor parent. The last backcross generation isthen selfed to give pure breeding progeny for the gene(s) beingtransferred.

Backcrossing can also be used in conjunction with pedigree breeding todevelop new inbred lines. For example, an F1 can be created that isbackcrossed to one of its parent lines to create a BC1. Progeny areselfed and selected so that the newly developed inbred has many of theattributes of the recurrent parent and yet several of the desiredattributes of the non-recurrent parent.

Recurrent selection is a method used in a plant breeding program toimprove a population of plants. The method entails individual plantscross pollinating with each other to form progeny which are then grown.The superior progeny are then selected by any number of methods, whichinclude individual plant, half sib progeny, full sib progeny, selfedprogeny and topcrossing. The selected progeny are cross pollinated witheach other to form progeny for another population. This population isplanted and again superior plants are selected to cross pollinate witheach other. Recurrent selection is a cyclical process and therefore canbe repeated as many times as desired. The objective of recurrentselection is to improve the traits of a population. The improvedpopulation can then be used as a source of breeding material to obtaininbred lines to be used in hybrids or used as parents for a syntheticcultivar. A synthetic cultivar is the resultant progeny formed by theintercrossing of several selected inbreds. Mass selection is a usefultechnique when used in conjunction with molecular marker enhancedselection as discussed earlier in this application.

The production of double haploids can also be used for the developmentof inbreds in a breeding program. Double haploids are produced by thedoubling of a set of chromosomes (1N) from a heterozygous plant toproduce a completely homozygous individual. For example, see Wan et al.,“Efficient Production of Doubled Haploid Plants Through ColchicineTreatment of Another-Derived Maize Callus”, Theoretical and AppliedGenetics, 77:889-892, 1989 and U.S. Patent Application 2003/0005479.This can be advantageous because the process omits the generations ofselfing needed to obtain a homozygous plant from a heterozygous source.

Haploid induction systems have been developed for various plants toproduce haploid tissues, plants and seed. The haploid induction systemcan produce haploid plants from any genotype by crossing a selected line(as female) with an inducer line. Such inducer lines for maize includeStock 6 (Coe, 1959, Am. Nat. 93:381-382; Sharkar and Coe, 1966, Genetics54:453-464), RWS (see Geiger, H. H. ‘Application of the in-vivo-haploidinduction in hybrid maize breeding’. [online], [retrieved 2008 Aug. 18].Retrieved from the Internet<https://www.uni-hohenheim.de/%7Eipspwww/350b/indexe.html#Project3>),KEMS (Deimling, Roeber, and Geiger, 1997, Vortr. Pflanzenzuchtg38:203-224), or KMS and ZMS (Chalyk, Bylich & Chebotar, 1994, MNL 68:47;Chalyk & Chebotar, 2000, Plant Breeding 119:363-364), and indeterminategametophyte (ig) mutation (Kermicle 1969 Science 166:1422-1424); thedisclosures of which are incorporated herein by reference.

Methods for obtaining haploid plants are also disclosed in Kobayashi, M.et al., Journ. of Heredity 71(1):9 14, 1980, Pollacsek, M., Agronomie(Paris) 12(3):247-251, 1992; Cho-Un-Haing et al., Journ. of Plant Biol.,1996, 39(3):185-188; Verdoodt, L., et al., February 1998, 96(2):294-300;Genetic Manipulation in Plant Breeding, Proceedings InternationalSymposium Organized by EUCARPIA, Sep. 8-13, 1985, Berlin, Germany;Chalyk et al., 1994, Maize Genet Coop. Newsletter 68:47; Chalyk, S. T.,1999, Maize Genet. Coop. Newsletter 73:53-54; Coe, R. H., 1959, Am. Nat.93:381-382; Deimling, S. et al., 1997, Vortr. Pflanzenzuchtg 38:203-204;Kato, A., 1999, J. Hered. 90:276 280; Lashermes, P. et al., 1988, Theor.Appl. Genet. 76:570-572 and 76:405-410; Tyrnov, V. S. et al., 1984,Dokl. Akad. Nauk. SSSR 276:735-738; Zabirova, E. R. et al., 1996,Kukuruza I Sorgo N4, 17-19; Aman, M. A., 1978, Indian J. Genet PlantBreed 38:452-457; Chalyk S. T., 1994, Euphytica 79:13-18; Chase, S. S.,1952, Agron. J. 44:263-267; Coe, E. H., 1959, Am. Nat. 93:381-382; Coe,E. H., and Sarkar, K. R., 1964 J. Hered. 55:231-233; Greenblatt, I. M.and Bock, M., 1967, J. Hered. 58:9-13; Kato, A., 1990, Maize Genet.Coop. Newsletter 65:109-110; Kato, A., 1997, Sex. Plant Reprod.10:96-100; Nanda, D. K. and Chase, S. S., 1966, Crop Sci. 6:213-215;Sarkar, K. R. and Coe, E. H., 1966, Genetics 54:453-464; Sarkar, K. R.and Coe, E. H., 1971, Crop Sci. 11:543-544; Sarkar, K. R. and Sachan J.K. S., 1972, Indian J. Agric. Sci. 42:781-786; Kermicle J. L., 1969,Mehta Yeshwant, M. R., Genetics and Molecular Biology, September 2000,23(3):617-622; Tahir, M. S. et al. Pakistan Journal of Scientific andIndustrial Research, August 2000, 43(4):258-261; Knox, R. E. et al.Plant Breeding, August 2000, 119(4):289-298; U.S. Pat. No. 5,639,951;the disclosures of which are incorporated herein by reference.

Hybrid seed production requires elimination or inactivation of pollenproduced by the female parent. Incomplete removal or inactivation of thepollen provides the potential for self-pollination. This inadvertentlyself-pollinated seed may be unintentionally harvested and packaged withhybrid seed. Also, because the male parent is grown next to the femaleparent in the field there is the very low probability that the maleselfed seed could be unintentionally harvested and packaged with thehybrid seed. Once the seed from the hybrid bag is planted, it ispossible to identify and select these self-pollinated plants. Theseself-pollinated plants will be genetically equivalent to one of theinbred lines used to produce the hybrid. Though the possibility ofinbreds being included in a hybrid seed bag exists, the occurrence isvery low because much care is taken by seed companies to avoid suchinclusions. It is worth noting that hybrid seed is sold to growers forthe production of grain and forage and not for breeding or seedproduction. By an individual skilled in plant breeding, these inbredplants unintentionally included in commercial hybrid seed can beidentified and selected due to their decreased vigor when compared tothe hybrid. Inbreds are identified by their less vigorous appearance forvegetative and/or reproductive characteristics, including shorter plantheight, small ear size, ear and kernel shape, cob color, or othercharacteristics.

Identification of these self-pollinated lines can also be accomplishedthrough molecular marker analyses. See, “The Identification of FemaleSelfs in Hybrid Maize: A Comparison Using Electrophoresis andMorphology”, Smith, J. S. C. and Wych, R. D., Seed Science andTechnology 14, pages 1-8 (1995), the disclosure of which is expresslyincorporated herein by reference. Through these technologies, thehomozygosity of the self pollinated line can be verified by analyzingallelic composition at various loci along the genome. Those methodsallow for rapid identification of the invention disclosed herein. Seealso, “Identification of Atypical Plants in Hybrid Maize Seed byPostcontrol and Electrophoresis” Sarca, V. et al., Probleme de GeneticaTeoritica si Aplicata Vol. 20 (1) pages 29-42.

Another form of commercial hybrid production involves the use of amixture of male sterile hybrid seed and male pollinator seed. Whenplanted, the resulting male sterile hybrid plants are pollinated by thepollinator plants. This method is primarily used to produce grain withenhanced quality grain traits, such as high oil, because desired qualitygrain traits expressed in the pollinator will also be expressed in thegrain produced on the male sterile hybrid plant. In this method thedesired quality grain trait does not have to be incorporated by lengthyprocedures such as recurrent backcross selection into an inbred parentline. One use of this method is described in U.S. Pat. Nos. 5,704,160and 5,706,603.

There are many important factors to be considered in the art of plantbreeding, such as the ability to recognize important morphological andphysiological characteristics, the ability to design evaluationtechniques for genotypic and phenotypic traits of interest, and theability to search out and exploit the genes for the desired traits innew or improved combinations.

The objective of commercial maize hybrid line development resulting froma maize plant breeding program is to develop new inbred lines to producehybrids that combine to produce high grain yields and superior agronomicperformance. One of the primary traits breeders seek is yield. However,many other major agronomic traits are of importance in hybridcombination and have an impact on yield or otherwise provide superiorperformance in hybrid combinations. Such traits include percent grainmoisture at harvest, relative maturity, resistance to stalk breakage,resistance to root lodging, grain quality, and disease and insectresistance. In addition, the lines per se must have acceptableperformance for parental traits such as seed yields, kernel sizes,pollen production, all of which affect ability to provide parental linesin sufficient quantity and quality for hybridization. These traits havebeen shown to be under genetic control and many if not all of the traitsare affected by multiple genes.

A breeder uses various methods to help determine which plants should beselected from the segregating populations and ultimately which inbredlines will be used to develop hybrids for commercialization. In additionto the knowledge of the germplasm and other skills the breeder uses, apart of the selection process is dependent on experimental designcoupled with the use of statistical analysis. Experimental design andstatistical analysis are used to help determine which plants, whichfamily of plants, and finally which inbred lines and hybrid combinationsare significantly better or different for one or more traits ofinterest. Experimental design methods are used to assess error so thatdifferences between two inbred lines or two hybrid lines can be moreaccurately determined. Statistical analysis includes the calculation ofmean values, determination of the statistical significance of thesources of variation, and the calculation of the appropriate variancecomponents. Either a five or one percent significance level iscustomarily used to determine whether a difference that occurs for agiven trait is real or due to the environment or experimental error. Oneof ordinary skill in the art of plant breeding would know how toevaluate the traits of two plant varieties to determine if there is nosignificant difference between the two traits expressed by thosevarieties. For example, see Fehr, Walt, Principles of CultivarDevelopment, pages 261-286 (1987) which is incorporated herein byreference. Mean trait values may be used to determine whether traitdifferences are significant, and preferably the traits are measured onplants grown under the same environmental conditions.

4. Optional Portable System

Using aspects of the process and apparatus described above, it may bepossible to take a portable laser to plants growing in a field orgreenhouse, ablate a small portion of a seed or leaf while on the plant,collect or gain access to specific tissue of the plant, and eitheranalyze the tissue there or collect it in a container correlated to anidentifier, and take it back to the lab for analysis.

5. Laser Engraving to Cut and Catch Cut Seed on Fly in Blister Pack

Another option is disclosed in FIG. 18. Laser 16 can be adjusted to acutting mode (e.g., an engraving mode) which can cut, dissect, orseparate completely through a seed by appropriate set up. This wouldallow a whole piece of the seed to be separated and then collected(e.g., well of a blister pack 100A). This could be automated andsynchronized so that plural seed can be serially cut up and theircut-off pieces collected. Correlation with the seed from which thepieces came can be maintained. One example is to simultaneously collecteach seed in a similarly indexed container (another blister pack 100B).

6. Bulk Segregate Analysis (BSA) of Multiple Seed

It can be possible to use similar methods and apparatus to conduct bulksegregate analysis (BSA) on multiple seed. A tissue removal tool couldbe set up to remove tissue from multiple seed in the same well, forexample a well 40 of a plate 18. The tissue from the multiple seed canthen be analyzed by BSA.

FIG. 18 could be used. The cut-off pieces could be collected frommultiple seed. Or multiple cut seed could be placed in the same well.Laser ablation could be set to cut up those multiple pieces to sizesthat can be used for BSA. Alternatively, a grinding mechanism couldgrind the seed into mixed fine particles.

One example of BSA is described in S Quarrie et al., “Bulk segregantanalysis with molecular markers and its use for improving droughtresistance in maize”, Journal of Experimental Botany, Vol 50, 1299-1306,Copyright© 1999 by Oxford University Press, which is incorporated byreference herein.

7. Simultaneous Sampling of Multiple Seed

Optionally, plural seed could be sampled simultaneously. One examplewould be to position plural seed in known locations and thensimultaneously remove or expose seed tissue, or a part of each seed.Ways to position plural seed in known locations is shown and described,for example, in U.S. application Ser. No. 12/336,084, filed Dec. 16,2008, which application is assigned to the owner of the presentapplication and incorporated by reference herein in its entirety. Oneway to ablate, remove, or expose seed tissue is with a laser (asdescribed herein). One way to ablate, remove, or expose seed tissuesimultaneously from a plurality of seed would be to either split asingle laser beam into multiple beams, each controlled to theappropriate location of a seed and at a power and with other operatingcharacteristics that ablate or remove seed tissue to create a sample(e.g., a chip from the seed of sufficient size to be useful foranalysis). There are a number of ways to split a laser beam for thispurpose. A few examples are discussed in U.S. Pat. Nos. 6,562,698 and6,327,090, which patents are incorporated by reference herein. Othersare also possible.

Alternatively, a single head could contain multiple lasers or one ormore laser beam splitters, with each laser configured to generate a beamor multiple beams that would ablate or remove tissue from a seed. Stillfurther, there could be multiple heads each with a laser to do so. Thesystem could control the generation and operation of each beam, as wellas how it is directed to its corresponding seed. One of skill in the artcan calibrate each laser or laser beam, how it is oriented or moved tooperating position, and the characteristics of operation to accomplishsimultaneous ablation or tissue, chip, or sample removal from multipleseed. For example, a laser configuration that could be used to achievethese embodiments is a galvo head incorporated into a laser.

1. A method for resource efficient selection of seed for production incommercial quantities or for research comprising: a. providing one ormore candidate seed; b. uniquely identifying each of the one or morecandidate seed; c. removing specific tissue or structure for a firstcandidate seed; d. performing seed specific analysis of i. the firstcandidate seed, and/or ii. the removed specific tissue or structure ofthe first candidate seed; e. storing data from the seed specificanalysis correlated to the unique identification of the first candidateseed; and f. using the data in an evaluation of whether the firstcandidate seed should be selected for production in commercialquantities or for research.
 2. The method of claim 1 wherein theevaluation compares the data, or conclusions derived from the data, tosimilar data or conclusions of other seed.
 3. The method of claim 1further comprising providing a plurality of candidate seed and removingspecific tissue or structure from a second candidate seed; performingseed specific analysis of the second candidate seed, and/or the removedspecific tissue or structure of the first candidate seed; storing datafrom the seed specific analysis correlated to the unique identificationof the second candidate seed; and using the data in an evaluation ofwhether the second candidate seed should be selected for production incommercial quantities or for research.
 4. The method of claim 3 whereinthe evaluation compares the data, or conclusions derived from the data,to similar data or conclusions relating to the first candidate seed. 5.The method of claim 1 wherein the step of removing tissue or structuredoes not materially affect viability or germination of the seed.
 6. Themethod of claim 1 wherein the step of removing comprises use of a laserbeam.
 7. The method of claim 6 further comprising isolating the seedfrom other seed.
 8. The method of claim 7 wherein isolating the seedcomprising placing the seed in a well or cavity having a bottom andsidewall.
 9. The method of claim 8 wherein the bottom and sidewall havesurface characteristics that diffuse or control reflection of the laserbeam.
 10. The method of claim 9 wherein the surface characteristicscomprise one or more of surface angle relative to the beam, surfacetexture, surface coating, or surface treatment.
 11. The method of claim1 further comprising automating one or more of steps a through e. 12.The method of claim 1 wherein the seed specific analysis comprises oneor more of genetic, chemical, or physical analysis, trait orcharacteristic analysis, and phenotype analysis.
 13. The method of claim1 wherein the seed comprises an agricultural seed.
 14. The method ofclaim 1 further comprising a plurality of candidate seed, each of thecandidate seed having at least one difference from the other comprisingone or more of genotype or phenotype.
 15. The method of claim 1 whereinthe seed comprises corn.
 16. The method of claim 15 wherein the tissueor structure comprises a portion of pericarp of the corn seed.
 17. Themethod of claim 16 wherein the portion of pericarp is just enough toexpose underlying tissues or structures of interest.
 18. The method ofclaim 17 wherein the underlying tissue or structure comprises an embryoor endosperm.
 19. The method of claim 1 further comprising placing theseed in a container in an indexed position correlated to the uniqueidentifier of the seed.
 20. A method for the removal of specific seedtissue or structure to enable seed specific analysis comprising: a.using a laser to non-destructively ablate, cut, or remove tissue orstructure from the seed; b. testing tissue or structure of the seed orremoved tissue or structure of the seed; and c. using results of thetesting in an evaluation of whether the seed should be selected forfurther use.
 21. The method of claim 20 wherein the further use isfurther use in research and development and in the production ofcommercial quantities of seed.
 22. A product, in commercial quantities,by the process of claim
 20. 23. The method of claim 20 furthercomprising controlling the laser to ablate, cut, or remove jut enough ofthe outer tissue or structure of the seed to expose underlying tissue orstructure of interest.
 24. The method of claim 20 further comprisingcutting off a portion of the seed using the laser.
 25. The method ofclaim 24 further comprising collecting the seed and the cut-off portionof the seed.
 26. A method to decrease time and space needed to sampletissue to allow selection of seed for production in commercialquantities or for research comprising: a. providing a plurality ofcandidate seed; b. uniquely identifying each of the candidate seed; c.removing specific tissue or structure for each candidate seed; d.performing seed specific analysis of each candidate seed or the removedtissue or structure; e. storing data from the seed specific analysiscorrelated to the unique identification of each candidate seed; and f.using the data in an evaluation of whether any candidate seed should beselected for production in commercial quantities or for research withoutgrowing the seed.
 27. The method of claim 26 wherein the step ofremoving specific tissue or structure is performed automatically on eachseed.
 28. The method of claim 27 wherein the automatic removingcomprises controlling a laser beam relative to each seed.
 29. The methodof claim 28 wherein the seed specific analysis comprises one or more ofgenetic, non-genetic, nanoscale, spectroscopic, phenotypic, or cellularlevel analysis.
 30. A method of testing, removing, or exposing specificseed structure or tissue of a seed comprising: a. non-destructivelyablating an outer tissue of the seed with a laser to expose underlyingtissue or structure; and b. directly testing the exposed underlyingtissue or structure for genetic content.
 31. The method of claim 30wherein the testing is for DNA, RNA, proteins, or lipids.
 32. The methodof claim 30 wherein the ablation is of a relatively small volume oftissue, including pericarp, of a corn kernel.
 33. The method of claim 30wherein the ablation is of a single seed contained in a cavity or wellhaving a surface texture, treatment, or coating that minimizesnon-diffusive laser reflection.
 34. The method of claim 30 wherein theablation is conducted on a plurality of seed, each in an individual wellor cavity.
 35. The method of claim 34 wherein the individual wells orcavities are formed in a single member.